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Crystal structure of O6-methylguanine methyltransferase Y91F variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WRJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2 M Potassium chloride, 0.05 M HEPES pH 7.5, 35% v/v Pentaerythritol propoxylate (5/4 PO/OH)
Crystal Properties Matthews coefficient Solvent content 2.18 43.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.102 α = 90 b = 52.839 β = 90 c = 61.837 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 2M 2016-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.13 40.17 99.9 0.066 0.069 0.019 0.998 26.1 12.7 59665
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.13 1.15 97.7 0.178 0.186 0.053 0.991 11.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1wrj 1.13 30.938 59597 2959 99.826 0.172 0.1712 0.1797 0.1966 0.2025 11.823
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.002 -0.001 -0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.411 r_dihedral_angle_4_deg 15.31 r_dihedral_angle_3_deg 12.54 r_dihedral_angle_1_deg 6.587 r_lrange_it 3.692 r_lrange_other 3.479 r_scangle_other 2.782 r_scangle_it 2.779 r_angle_refined_deg 2.176 r_scbond_other 1.922
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.411 r_dihedral_angle_4_deg 15.31 r_dihedral_angle_3_deg 12.54 r_dihedral_angle_1_deg 6.587 r_lrange_it 3.692 r_lrange_other 3.479 r_scangle_other 2.782 r_scangle_it 2.779 r_angle_refined_deg 2.176 r_scbond_other 1.922 r_scbond_it 1.921 r_mcangle_it 1.664 r_mcangle_other 1.663 r_angle_other_deg 1.57 r_mcbond_it 1.179 r_mcbond_other 1.178 r_symmetry_nbd_refined 0.312 r_nbd_other 0.229 r_nbd_refined 0.225 r_nbtor_refined 0.192 r_symmetry_nbd_other 0.182 r_xyhbond_nbd_refined 0.168 r_symmetry_xyhbond_nbd_refined 0.156 r_chiral_restr 0.121 r_symmetry_nbtor_other 0.09 r_bond_refined_d 0.018 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1235 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 5
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing